v3.4
Steven N. Hart, Ph.D
9/30/2019
all_annotations = read.csv('sources/v3.4a.out',header=TRUE, stringsAsFactors = FALSE, sep="\t")
#Get BayesDel
bd = read.csv('sources/BayesDel_nsfp33a_noAF.tsv',header=TRUE, sep="\t", skip = 132)
bd$ID=NULL
names(bd) =c("Chr", "Pos", "Ref", "Alt", "BayesDel")
all_annotations = merge(all_annotations, bd, all.x=TRUE)
rm(bd)
#Get AlignGVGD
agvgd = read.csv('sources/alignGvgd.tsv', header=TRUE, sep="\t", stringsAsFactors = FALSE)
names(agvgd) =c("Chr", "Pos", "Ref", "Alt", "AlignGVGDPrior")
all_annotations = merge(all_annotations, agvgd, all.x=TRUE)
rm(agvgd)
for (j in names(all_annotations)[6:ncol(all_annotations)]){
if (typeof(all_annotations[,j]) == 'character'){
#all_annotations[,j] = vapply(strsplit(all_annotations[,j],"\\|"), `[`, 1, FUN.VALUE=character(1)) %>% as.numeric()
# Get the maximum score
all_annotations[,j] = suppressWarnings(sapply(strsplit(all_annotations[,j], "\\|"), function(x) (max(x,na.rm = TRUE))) %>% as.numeric())
}
}
all_annotations = all_annotations %>%
filter(AApos>0)
keep = names(all_annotations)[-grep("Rankscore",names(all_annotations))]
all_annotations = all_annotations[,keep]
all_annotations = all_annotations %>%
mutate(Variant = paste(Chr,Pos,Ref,Alt,sep='_'))
rm(keep, j)
#glimpse(all_annotations)Plot all predictions
Set some useful functions
# Create a filter to remove nything not in the BRCT/RING domains of BRCA1 and the DNA binding domain of BRCA2
filter_to_target_regions = function(d, variant_search = FALSE, l = links)
{
RING_prot = c(1, 109)
BRCT_prot = c(1642, 1855)
DNABD_prot = c(2479, 3192)
if(variant_search == TRUE){
d$Variant = as.character(d$Variant)
d = merge(d, l)
}
#Filter BRCA1 variants
d$X.CHROM = as.numeric(d$X.CHROM)
d$AApos = as.numeric(d$AApos)
BRCA1_keep_idx = which(
d$X.CHROM == 17 & (
dplyr::between(d$AApos, RING_prot[1], RING_prot[2]) | dplyr::between(d$AApos,BRCT_prot[1], BRCT_prot[2])
)
)
BRCA2_keep_idx = which(d$X.CHROM == 13 & dplyr::between(d$AApos, DNABD_prot[1], DNABD_prot[2]))
d = d[c(BRCA1_keep_idx,BRCA2_keep_idx),]
d = distinct(d, Variant, .keep_all = TRUE)
rm(RING_prot, BRCT_prot, DNABD_prot, BRCA1_keep_idx, BRCA2_keep_idx)
return(d)
}
### Define the MCC function
mcc <- function(predicted, actual)
{
TP <- sum(actual == "Damaging" & predicted == "Damaging")
TN <- sum(actual == "Neutral" & predicted == "Neutral")
FP <- sum(actual == "Neutral" & predicted == "Damaging")
FN <- sum(actual == "Damaging" & predicted == "Neutral")
mcc <- ((TP*TN) - (FP*FN)) / sqrt((as.numeric(TP + FP)*as.numeric(TP + FN)*as.numeric(TN + FP)*as.numeric(TN + FN)))
rm(TP, TN, FP, FN)
return(round(mcc, digits = 3))
}
links = all_annotations %>%
mutate(Variant = paste(Chr,Pos, Ref, Alt, sep = "_")) %>%
mutate(X.CHROM=Chr, POS=Pos, REF=Ref, ALT=Alt) %>%
select(X.CHROM, AApos, Variant )Load all functional data
#Read in our data
neutral_list = read.csv(paste0(wd, "/sources/neutral.list"),sep = "\t",header = FALSE, stringsAsFactors = FALSE)
damaging_list = read.csv(paste0(wd, "/sources/deleterious.list"),sep = "\t",header = FALSE, stringsAsFactors = FALSE)
Hart_df = rbind(neutral_list,damaging_list)
names(Hart_df) = c("Gene","Variant","Call", "Source")
Hart_df = filter_to_target_regions(Hart_df, variant_search = TRUE)
rm(neutral_list, damaging_list)#######################################################################################################################################
#Read in Starita
#Get data
Starita = read.csv(paste0(wd, '/sources/Starita.tsv'),header = TRUE,
sep = "\t", stringsAsFactors = FALSE,
na.strings = c('.'))
HDR_damaging_max = 0.33
HDR_neutral_min = 0.77
Starita = Starita %>%
filter(HDR <= HDR_damaging_max | HDR >= HDR_neutral_min)
Starita_df = data.frame(
Variant = as.character(Starita$cpra),
Gene = 'BRCA1',
Call = ifelse(Starita$HDR <= HDR_damaging_max, "Damaging", 'Neutral' )
)
Starita_df = na.omit(Starita_df)
Starita_df = Starita_df %>%
select(Gene, Variant, Call) %>%
mutate(Source = "Starita et al., 2015")
Starita_df = filter_to_target_regions(Starita_df, variant_search = TRUE)
rm(Starita, HDR_damaging_max, HDR_neutral_min)#######################################################################################################################################
#Read in Fernandes
#Get data
Fernandes = read.csv(paste0(wd, "/sources/Fenandez.tsv"), header = TRUE,
sep = "\t", stringsAsFactors = FALSE)
#Remove WT and splic variants
omit = Fernandes$variant[grep('del|\\+|WT|\\/|ins',Fernandes$variant)]
Fernandes = Fernandes %>%
filter(!variant %in% omit) %>%
filter(IARC %in% c(0,1,4,5)) %>%
mutate(Call = ifelse(IARC > 2, "Damaging", "Neutral"), Gene = 'BRCA1') %>%
select(Gene, Variant, Call) %>%
mutate(Source = "Fernandes et al., 2019")
Fernandes_df = filter_to_target_regions(Fernandes, variant_search = TRUE)
rm(Fernandes, omit)#######################################################################################################################################
#Read in Findlay
#Get data
Findaly = read.csv(paste0(wd, '/sources/Findlay.tsv'), header = TRUE,sep = "\t",
stringsAsFactors = FALSE, na.strings = c('','NA','.'))
# Exclude splicing (1/28)
Findaly = Findaly %>%
filter(Type %in% c('missense_variant'), Call %in% c('Deleterious','Neutral'))
Fin_df = data.frame(
Gene = Findaly$Gene,
Variant = Findaly$CPRA,
Call = Findaly$func.class,
Score = Findaly$function.score.mean,
Seen = Findaly$AlreadySeen)
Findlay_df = Fin_df %>%
filter(Seen == 0)
Findlay_df$Call = ifelse(Findlay_df$Call == 'FUNC', 'Neutral', 'Damaging')
Findlay_df = Findlay_df %>%
select(Gene, Variant, Call) %>%
mutate(Source = "Findlay et al., 2018")
Findlay_df = filter_to_target_regions(Findlay_df, variant_search = TRUE)
rm(Fin_df, Findaly)#######################################################################################################################################
# Combine experimental datasets
experimental_data = rbind(Hart_df, Fernandes_df, Starita_df, Findlay_df)
d = as.data.frame(table(experimental_data$Gene, experimental_data$Call, experimental_data$Source))
names(d) = c('Gene', 'Call', 'Source', 'RawCount')
experimental_data = distinct(experimental_data, Gene, Variant, .keep_all = TRUE)
e = as.data.frame(table(experimental_data$Gene, experimental_data$Call, experimental_data$Source))
names(e) = c('Gene', 'Call', 'Source', 'FilteredCount')
Counts = cbind(d, e$FilteredCount)
names(Counts)[length(names(Counts))] = 'FilteredCount'
rm(Hart_df, Fernandes_df, Starita_df, Findlay_df)
table(experimental_data$Source, experimental_data$Call,experimental_data$Gene)## , , = BRCA1
##
##
## Damaging Neutral
## Fernandes et al., 2019 0 16
## Findlay et al., 2018 55 259
## Guidugli et al., 2014 0 0
## Guidugli et al., 2018 0 0
## Hart et al, 2018 1 2
## Lee et al., 2010 14 13
## Lindor et al., 2012 0 0
## Starita et al., 2015 11 1044
## This paper 0 0
## Woods et al., 2016 3 36
##
## , , = BRCA2
##
##
## Damaging Neutral
## Fernandes et al., 2019 0 0
## Findlay et al., 2018 0 0
## Guidugli et al., 2014 4 0
## Guidugli et al., 2018 38 48
## Hart et al, 2018 16 47
## Lee et al., 2010 0 0
## Lindor et al., 2012 9 18
## Starita et al., 2015 0 0
## This paper 7 15
## Woods et al., 2016 0 0table(experimental_data$Call,experimental_data$Gene)##
## BRCA1 BRCA2
## Damaging 84 74
## Neutral 1370 128More custom functions
prepare_inputs = function(data = experimental_data,
annotations = all_annotations,
gene = 'BRCA1',
sources = NULL){
s = NULL
if ('Hart' %in% sources){s = c("This paper", "Guidugli et al., 2018",
"Hart et al, 2018", "Lee et al., 2010",
"Lindor et al., 2012", "Woods et al., 2016",
"Guidugli et al., 2014")}
if ('Fernandes' %in% sources){s = c(s, 'Fernandes et al., 2019')}
if ('Starita' %in% sources){s = c(s, 'Starita et al., 2015')}
if ('Findlay' %in% sources){s = c(s, 'Findlay et al., 2018')}
# if sources = PATH, then take all pathogenic variants from all studies and benign from our study
if(is.null(s)){
data = data %>%
filter(Gene == gene)
}else{
# Filter to known results for a specific gene
data = data %>%
filter(Source %in% s, Gene == gene)
}
data = distinct(data, Gene, Variant, .keep_all = TRUE)
#Merge to get annotations
data = merge(data,
annotations,
all.x = TRUE,
by = 'Variant')
# Sort list randomly
data = sample(data)
if ('Gene.x' %in% names(data)){ data = data %>% mutate(Gene = Gene.x, Gene.x=NULL, Gene.y=NULL)}
if ('AApos.x' %in% names(data)){ data = data %>% mutate(AApos = AApos.x, AApos.x=NULL, AApos.y=NULL)}
if ('X.CHROM.x' %in% names(data)){ data = data %>% mutate(X.CHROM = X.CHROM.x, X.CHROM.x=NULL, X.CHROM.y=NULL)}
return(data)
}
split_data = function(known_scores, validation_fraction = 0.2 ){
set.seed(999)
known_scores$Call = as.factor(known_scores$Call)
num_predictions = nrow(known_scores)
#Create training testing and validation
Neutral_idx = which(known_scores$Call == 'Neutral')
Damaging_idx = which(known_scores$Call == 'Damaging')
n_train_idx = sample(Neutral_idx, size = length(Neutral_idx) * 0.8)
d_train_idx = sample(Damaging_idx, size = length(Damaging_idx) * 0.8)
# Subset to training and validation
idx = c(n_train_idx, d_train_idx)
#Shuffle randomly
idx = sample(idx)
train = known_scores[idx,]
test = known_scores[-idx,]
splits = NULL
splits$test = NULL
splits$train = NULL
splits$train = train
splits$test = test
return(splits)
}
k_fold_split_data = function(known_scores, k=10 ){
set.seed(999)
known_scores$Call = as.factor(known_scores$Call)
num_predictions = nrow(known_scores)
#Create training testing and validation
Neutral_idx = which(known_scores$Call == 'Neutral')
Neutral_fold = createFolds(Neutral_idx, k = k, list = FALSE)
Damaging_idx = which(known_scores$Call == 'Damaging')
Damaging_fold = createFolds(Damaging_idx, k = k, list = FALSE)
# Subset to training and validation
idx_f = c(Neutral_fold, Damaging_fold)
known_scores$Fold = idx_f
splits = sample(known_scores)
return(splits)
}
train_model = function(splits, k_=NULL, Gene = 'BRCA1'){
knitr::opts_chunk$set(echo=FALSE)
h2o.init(min_mem_size = "16g", max_mem_size = "32g", nthreads = 20)
train = as.h2o(splits$train)
all_h2o_models = h2o.automl(x = COLUMNS, y = "Call",
training_frame = train,
keep_cross_validation_predictions = TRUE,
nfolds = 5,
max_runtime_secs = 3600,
sort_metric = 'mean_per_class_error',
stopping_metric = 'mean_per_class_error',
seed = 100)
knitr::opts_chunk$set(echo=TRUE)
#Save the model
best_model = h2o.saveModel(object = all_h2o_models@leader,path = "results/",force = TRUE)
best_model
all_h2o_models
# Load model
model_out = h2o.loadModel(best_model)
model_vi = as.data.frame(all_h2o_models@leader@model$variable_importances)
threshold = h2o.find_threshold_by_max_metric(h2o.performance(model_out), 'absolute_mcc')
my_list = list('all_h2o_models' = all_h2o_models, 'best_model' = best_model,
'model' = model_out, 'vi' = model_vi, 'threshold' = threshold)
return(my_list)
}
test_model = function(splits, model, threshold = NULL){
knitr::opts_chunk$set(echo=FALSE)
h2o.init(min_mem_size = "16g", max_mem_size = "32g", nthreads = 1)
test = as.h2o(splits$test)
pred = h2o.predict(model,
newdata = test,
threshold = threshold)
knitr::opts_chunk$set(echo=TRUE)
pred = as.data.frame(pred)
#Edit prediction based on previous threshold
final_result = cbind(splits$test, pred)
cm = confusionMatrix(final_result$predict,final_result$Call, positive = 'Damaging')
m = mcc(final_result$predict,final_result$Call)
my_list = list('result' = final_result, 'cm' = cm, 'MCC' = m)
return(my_list)
}
apply_model_to_gene = function(model = model, threshold = threshold,
gene = 'BRCA1', annotations = all_annotations){
#Run model on each gene
tmp = annotations %>%
filter(Genename == gene)
pred = h2o.predict(model, newdata = as.h2o(tmp), threshold = threshold)
pred = as.data.frame(pred)
tmp$Prediction = pred$predict
tmp$`BRCA-ML` = pred$Damaging
tmp$Neut = pred$Neutral
return(tmp)
}
plot_full_gene = function(data, title, splits = splits, model_name='BRCA-ML', t_=NULL){
#Pull out training, validation, & testing variants to plot
if(length(splits$train)){
variants = splits$train %>%
select(AApos, Call)
variants = rbind(variants,splits$test %>%
select(AApos, Call)
)
}else{
variants = NULL
}
tmp = data[,c("Genename","BRCA-ML","AApos","Prediction")]
tmp$Model = model_name
names(tmp) = c("Gene","Score","AApos","Prediction","Model")
tmp$Prediction = as.character(tmp$Prediction)
if (!is.null(t_)){tmp = tmp %>% mutate(Prediction = ifelse(Score > t_, 'Damaging', 'Neutral'))}
p = tmp %>%
ggplot(aes(x = AApos,y = Score, colour = Prediction)) +
geom_point(size = 0.2) +
#facet_grid(Model ~ Gene, scales = 'free') +
geom_smooth(aes(x = AApos,y = Score), inherit.aes = FALSE) +
ggtitle(title) +
theme(legend.position="none")
if(length(splits$train)){
p = p + geom_rug(
aes(x=AApos, colour=Call, alpha = 1/2),
inherit.aes = FALSE,
sides = "b",
data = variants)
}
return(p)
}Define columns to TRAIN on
models = read.csv(paste0(wd, '/sources/base_thresholds'), header = FALSE, sep="\t", stringsAsFactors = FALSE)
COLUMNS = models$V1Run the training
#BRCA1
b1_input = prepare_inputs(gene = 'BRCA1')
b1_DATA_SPLITS = split_data(b1_input)
b1_TRAINED_DATA = train_model(b1_DATA_SPLITS)##
## H2O is not running yet, starting it now...
##
## Note: In case of errors look at the following log files:
## /tmp/RtmpnTasxs/h2o_m087494_started_from_r.out
## /tmp/RtmpnTasxs/h2o_m087494_started_from_r.err
##
##
## Starting H2O JVM and connecting: . Connection successful!
##
## R is connected to the H2O cluster:
## H2O cluster uptime: 1 seconds 385 milliseconds
## H2O cluster timezone: CST6CDT
## H2O data parsing timezone: UTC
## H2O cluster version: 3.22.1.1
## H2O cluster version age: 9 months and 2 days !!!
## H2O cluster name: H2O_started_from_R_m087494_whe707
## H2O cluster total nodes: 1
## H2O cluster total memory: 28.44 GB
## H2O cluster total cores: 80
## H2O cluster allowed cores: 20
## H2O cluster healthy: TRUE
## H2O Connection ip: localhost
## H2O Connection port: 54321
## H2O Connection proxy: NA
## H2O Internal Security: FALSE
## H2O API Extensions: XGBoost, Algos, AutoML, Core V3, Core V4
## R Version: R version 3.5.2 (2018-12-20)
##
##
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|==============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================| 100%# GBM_grid_1_AutoML_20190920_074644_model_55
b1_TESTED_DATA = test_model(b1_DATA_SPLITS, b1_TRAINED_DATA$model, threshold = b1_TRAINED_DATA$threshold)## Connection successful!
##
## R is connected to the H2O cluster:
## H2O cluster uptime: 53 minutes 35 seconds
## H2O cluster timezone: CST6CDT
## H2O data parsing timezone: UTC
## H2O cluster version: 3.22.1.1
## H2O cluster version age: 9 months and 2 days !!!
## H2O cluster name: H2O_started_from_R_m087494_whe707
## H2O cluster total nodes: 1
## H2O cluster total memory: 27.84 GB
## H2O cluster total cores: 80
## H2O cluster allowed cores: 20
## H2O cluster healthy: TRUE
## H2O Connection ip: localhost
## H2O Connection port: 54321
## H2O Connection proxy: NA
## H2O Internal Security: FALSE
## H2O API Extensions: XGBoost, Algos, AutoML, Core V3, Core V4
## R Version: R version 3.5.2 (2018-12-20)
##
##
|
| | 0%
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|==============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================| 100%
##
|
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|==============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================| 100%b1_PREDICTIONS = apply_model_to_gene(model = b1_TRAINED_DATA$model,
gene = 'BRCA1',
threshold = b1_TRAINED_DATA$threshold)##
|
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|==============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================| 100%
##
|
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|==============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================| 100%b1_PLOTS = plot_full_gene(b1_PREDICTIONS,
'BRCA1',
splits = b1_DATA_SPLITS,
t_ = b1_TRAINED_DATA$threshold )
#BRCA2
b2_input = prepare_inputs(gene = 'BRCA2')
b2_DATA_SPLITS = split_data(b2_input)
b2_TRAINED_DATA = train_model(b2_DATA_SPLITS)## Connection successful!
##
## R is connected to the H2O cluster:
## H2O cluster uptime: 53 minutes 40 seconds
## H2O cluster timezone: CST6CDT
## H2O data parsing timezone: UTC
## H2O cluster version: 3.22.1.1
## H2O cluster version age: 9 months and 2 days !!!
## H2O cluster name: H2O_started_from_R_m087494_whe707
## H2O cluster total nodes: 1
## H2O cluster total memory: 27.84 GB
## H2O cluster total cores: 80
## H2O cluster allowed cores: 20
## H2O cluster healthy: TRUE
## H2O Connection ip: localhost
## H2O Connection port: 54321
## H2O Connection proxy: NA
## H2O Internal Security: FALSE
## H2O API Extensions: XGBoost, Algos, AutoML, Core V3, Core V4
## R Version: R version 3.5.2 (2018-12-20)
##
##
|
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|==============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================| 100%
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|======================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= | 92%
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|
|==============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================| 100%# XGBoost_grid_1_AutoML_20190920_084013_model_2
b2_TESTED_DATA = test_model(b2_DATA_SPLITS, b2_TRAINED_DATA$model, threshold = b2_TRAINED_DATA$threshold)## Connection successful!
##
## R is connected to the H2O cluster:
## H2O cluster uptime: 1 hours 34 minutes
## H2O cluster timezone: CST6CDT
## H2O data parsing timezone: UTC
## H2O cluster version: 3.22.1.1
## H2O cluster version age: 9 months and 2 days !!!
## H2O cluster name: H2O_started_from_R_m087494_whe707
## H2O cluster total nodes: 1
## H2O cluster total memory: 27.69 GB
## H2O cluster total cores: 80
## H2O cluster allowed cores: 20
## H2O cluster healthy: TRUE
## H2O Connection ip: localhost
## H2O Connection port: 54321
## H2O Connection proxy: NA
## H2O Internal Security: FALSE
## H2O API Extensions: XGBoost, Algos, AutoML, Core V3, Core V4
## R Version: R version 3.5.2 (2018-12-20)
##
##
|
| | 0%
|
|==============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================| 100%
##
|
| | 0%
|
|==============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================| 100%b2_PREDICTIONS = apply_model_to_gene(model = b2_TRAINED_DATA$model,
gene = 'BRCA2',
threshold = b2_TRAINED_DATA$threshold)##
|
| | 0%
|
|==============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================| 100%
##
|
| | 0%
|
|==============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================| 100%b2_PLOTS = plot_full_gene(b2_PREDICTIONS,
'BRCA2',
splits = b2_DATA_SPLITS,
t_ = b2_TRAINED_DATA$threshold )Make functions to determine cutoff for other missense predictors
get_res = function(input_data, model){
# Make a df that merges the experimental results with predictors
tmp = input_data$train[,c('Variant',model)]
tmp = merge(tmp, experimental_data)
tmp = tmp[,c('Call',model)]
roc_obj <- roc(tmp$Call, tmp[,model])
d = t(as.data.frame(coords(roc_obj, "best", ret=c("threshold","sensitivity", "specificity", "tp", "tn", "fp", "fn"))))
rownames(d)=NULL
d = as.data.frame(d)
d$mcc = ((d$tp*d$tn) - (d$fp * d$fn)) / sqrt((as.numeric(d$tp + d$fp)*as.numeric(d$tp + d$fn)*as.numeric(d$tn + d$fp)*as.numeric(d$tn + d$fn)))
d$model = model
pr_1 =NULL
# Add precision recall
idx = which(tmp$Call=='Neutral')
tryCatch(
{
pr_1 = pr.curve(
scores.class0 = tmp[-idx, model],
scores.class1 = tmp[idx, model],
curve=TRUE, sorted = FALSE)
},
error = function(cond){
pr_1 = NULL
})
if (is.null(pr_1)){
proc = NULL
proc$V1 = 0
proc$V2 = 0
proc$V3 = 0
proc$Model = model
d$PRauc = 0
}else{
d$PRauc = pr_1$auc.integral
proc = pr_1$curve %>% as.data.frame()
proc$Model = model
}
my_list = list('roc' = roc_obj, 'res' = d, 'proc' = proc)
rm(d, tmp)
return(my_list)
}
compute_optimal = function(input_data=b1_DATA_SPLITS){
RES = NULL
ROC = NULL
PROC = NULL
for (model in models$V1){
l = get_res(input_data, model)
RES = rbind(RES, l$res)
d1 = data.frame(sensitivities=l$roc$sensitivities, specificities=l$roc$specificities, auc = as.numeric(l$roc$auc))
d1$Model = model
ROC = rbind(ROC, d1)
# Add PROC
tryCatch(
{PROC = rbind(PROC, l$proc)},
error = function(cond){
PROC = PROC
}
)
}
my_list = list('RES' = RES, 'ROC' = ROC, 'PROC' = PROC)
return(my_list)
}Compute for BRCA1
res_roc_1 = compute_optimal()#Add in metrics from our current model
tmp = b1_PREDICTIONS %>%
filter(Variant %in% experimental_data$Variant)
tmp = merge(tmp, experimental_data)
tmp = tmp[,c('Call','BRCA-ML')]
roc_obj <- roc(tmp$Call, tmp$`BRCA-ML`)
d = t(as.data.frame(coords(roc_obj, "best", ret=c("threshold","sensitivity", "specificity","tp","tn","fp","fn"))))
rownames(d)=NULL
d = as.data.frame(d)
d$mcc = ((d$tp*d$tn) - (d$fp * d$fn)) / sqrt((as.numeric(d$tp + d$fp)*as.numeric(d$tp + d$fn)*as.numeric(d$tn + d$fp)*as.numeric(d$tn + d$fn)))
d$model = 'BRCA-ML'
# Add precision recall
idx = which(tmp$Call=='Neutral')
pr_1 = pr.curve(
scores.class0 = tmp$`BRCA-ML`[-idx],
scores.class1 = tmp$`BRCA-ML`[idx],
curve=TRUE,sorted = FALSE)
d$PRauc = pr_1$auc.integral
res_roc_1$RES = rbind(res_roc_1$RES, d)
## Start getting curve info
d1 = data.frame(sensitivities=roc_obj$sensitivities, specificities=roc_obj$specificities, auc = as.numeric(roc_obj$auc))
d1$Model='BRCA-ML'
d2 = pr_1$curve %>% as.data.frame()
d2$Model = 'BRCA-ML'
res_roc_1$ROC = rbind(res_roc_1$ROC, d1)
res_roc_1$PROC = rbind(res_roc_1$PROC, d2)
rm(d,d1,d2, tmp)
p1 = res_roc_1$ROC %>%
#filter(auc > 0.8) %>%
#ggplot(aes(y=sensitivities, x=1-specificities, color = paste0(Model,"=", round(auc,3)))) +
ggplot(aes(y=sensitivities, x=1-specificities, color = Model)) +
geom_line() +
scale_fill_brewer(palette="Paired") +
labs(color='Model') +
xlab("Specificity") +
ylab("Sensitivity") +
ggtitle('BRCA1') +
theme(legend.position = "none")
p1 + theme(legend.position="right")
#ggsave(filename = paste0(wd,"/results/BRCA1_ROC.png"), width = 12, height = 6, units = "in", dpi = 300)Compute for BRCA2
res_roc_2 = compute_optimal(input_data=b2_DATA_SPLITS)
#Add in metrics from our current model
tmp = b2_PREDICTIONS %>%
filter(Variant %in% experimental_data$Variant)
tmp = merge(tmp, experimental_data)
tmp = tmp[,c('Call','BRCA-ML')]
roc_obj <- roc(tmp$Call, tmp$`BRCA-ML`)
d = t(as.data.frame(coords(roc_obj, "best", ret=c("threshold","sensitivity", "specificity","tp","tn","fp","fn"))))
rownames(d)=NULL
d = as.data.frame(d)
d$mcc = ((d$tp*d$tn) - (d$fp * d$fn)) / sqrt((as.numeric(d$tp + d$fp)*as.numeric(d$tp + d$fn)*as.numeric(d$tn + d$fp)*as.numeric(d$tn + d$fn)))
d$model = 'BRCA-ML'
# Add precision recall
idx = which(tmp$Call=='Neutral')
pr_1 = pr.curve(
scores.class0 = tmp$`BRCA-ML`[-idx],
scores.class1 = tmp$`BRCA-ML`[idx],
curve=TRUE,sorted = FALSE)
d$PRauc = pr_1$auc.integral
res_roc_2$RES = rbind(res_roc_2$RES, d)
d1 = data.frame(sensitivities=roc_obj$sensitivities, specificities=roc_obj$specificities, auc = as.numeric(roc_obj$auc))
d1$Model='BRCA-ML'
d2 = pr_1$curve %>% as.data.frame()
d2$Model='BRCA-ML'
res_roc_2$ROC = rbind(res_roc_2$ROC, d1)
res_roc_2$PROC = rbind(res_roc_2$PROC, d2)
rm(d,d1,tmp)
p2 = res_roc_2$ROC %>%
#filter(auc > 0.8) %>%
#ggplot(aes(y=sensitivities, x=1-specificities, color = paste0(Model,"=", round(auc,3)))) +
ggplot(aes(y=sensitivities, x=1-specificities, color = Model)) +
geom_line() +
scale_fill_brewer(palette="Paired") +
labs(color='Model') +
xlab("Specificity") +
ylab("Sensitivity") +
ggtitle('BRCA2')
p2 + theme(legend.position="right")
#ggsave(filename = paste0(wd,"/results/BRCA2_ROC.png"), width = 12, height = 6, units = "in", dpi = 300)Make a combined image
ggarrange(p1, p2,ncol=2, nrow=1, common.legend = TRUE, legend = "bottom")
#ggsave(filename = paste0(wd,"/results/Combined_ROC.png"), width = 16, height = 8, units = "in", dpi = 300)Make PR Curves
res_roc_1$PROC$Gene='BRCA1'
res_roc_2$PROC$Gene='BRCA2'
PROC = rbind(res_roc_1$PROC, res_roc_2$PROC)
p3 = PROC %>%
filter(Gene == 'BRCA1') %>%
ggplot(aes(x=V1, y=V2, color=Model)) +
geom_line() +
facet_grid(. ~ Gene) +
theme(legend.position = "none") +
ylab('Precision') +
xlab("Recall")
p3
p4 = PROC %>%
filter(Gene == 'BRCA2') %>%
ggplot(aes(x=V1, y=V2, color=Model)) +
geom_line() +
facet_grid(. ~ Gene) +
theme(legend.position = "right")+
ylab('Precision') +
xlab("Recall")
p4
ggarrange(p3, p4, common.legend = TRUE, legend = "bottom")
#ggsave(filename = paste0(wd,"/results/Combined_PROC.png"), width = 16, height = 8, units = "in", dpi = 300)All together now
ggarrange(p1, p2, p3, p4, common.legend = TRUE, legend = "right")
ggsave(filename = paste0(wd,"/results/Combined_PROC_ROC.png"), width = 14, height = 8, units = "in", dpi = 300)Make pair plot
tmp = b1_PREDICTIONS %>%
select(AApos, `BRCA-ML`, BayesDel) %>%
mutate(Gene='BRCA1')
tmp2 = b2_PREDICTIONS %>%
select(AApos, `BRCA-ML`, BayesDel) %>%
mutate(Gene='BRCA2')
tmp = rbind(tmp, tmp2)
tmp = tmp %>%
gather(key = "Model", value = 'Value', `BRCA-ML`:BayesDel)
## Assign damaging score
tmp$Prediction='Neutral'
idx1 = which(tmp$Gene == 'BRCA1' & tmp$Value >= b1_TRAINED_DATA$threshold & tmp$Model == 'BRCA-ML')
idx2 = which(tmp$Gene == 'BRCA2' & tmp$Value >= b2_TRAINED_DATA$threshold & tmp$Model == 'BRCA-ML')
bd_thresh = res_roc_1$RES %>% filter(model=='BayesDel') %>% select(threshold) %>% as.numeric()
idx3 = which(tmp$Gene == 'BRCA1' & tmp$Value >= bd_thresh & tmp$Model == 'BayesDel')
bd_thresh = res_roc_2$RES %>% filter(model=='BayesDel') %>% select(threshold) %>% as.numeric()
idx4 = which(tmp$Gene == 'BRCA2' & tmp$Value >= bd_thresh & tmp$Model == 'BayesDel')
tmp$Prediction[c(idx1,idx2,idx3,idx4)] = 'Damaging'
rm(idx1,idx2,idx3,idx4, bd_thresh)
tmp %>%
ggplot(aes(x=AApos, y=Value, color=Prediction)) +
geom_point(size=0.5) +
geom_smooth(aes(x = AApos,y = Value), inherit.aes = FALSE) +
facet_wrap(~Model+Gene, scales = "free", ncol=2) +
theme(legend.position = "bottom")
ggsave(filename = paste0(wd,"/results/PairPlot.png"), width = 14, height = 8, units = "in", dpi = 300)Print AUPROC
res_roc_1$RES$Gene='BRCA1'
res_roc_2$RES$Gene='BRCA2'
tmp = rbind(res_roc_1$RES, res_roc_2$RES)
tmp %>%
dplyr::arrange(1-mcc)## threshold sensitivity specificity tp tn fp fn mcc model PRauc Gene
## 1 0.50463650 0.96093750 0.86486486 123 64 10 5 0.83897033 BRCA-ML 0.95635057 BRCA2
## 2 0.07296303 0.94014599 0.97619048 1288 82 2 82 0.67583101 BRCA-ML 0.85823057 BRCA1
## 3 0.29937650 0.85294118 0.83050847 87 49 10 15 0.67290966 BayesDel 0.82886006 BRCA2
## 4 0.28744524 0.76530612 0.84745763 75 50 9 23 0.59501928 MCapScore 0.00000000 BRCA2
## 5 0.66550000 0.66666667 0.93220339 68 55 4 34 0.58035996 RevelScore 0.77389379 BRCA2
## 6 0.80550000 0.80392157 0.77966102 82 46 13 20 0.57173482 Vest3Score 0.68749167 BRCA2
## 7 0.73920000 0.71568627 0.86440678 73 51 8 29 0.55903147 MetalrScore 0.76499182 BRCA2
## 8 0.76750000 0.81578947 0.72222222 62 39 15 14 0.53952565 MutpredScore 0.00000000 BRCA2
## 9 0.36070000 0.60784314 0.93220339 62 55 4 40 0.52908262 MetasvmScore 0.77965613 BRCA2
## 10 -2.43500000 0.89215686 0.57627119 91 34 25 11 0.50296033 FathmmScore 0.23772313 BRCA2
## 11 0.98750000 0.55882353 0.93220339 57 55 4 45 0.48771541 Polyphen2HvarScore 0.60575001 BRCA2
## 12 0.81084154 0.76470588 0.69491525 78 41 18 24 0.45137114 EigenRaw 0.70829596 BRCA2
## 13 0.73882692 0.69607843 0.72881356 71 43 16 31 0.41079878 EigenPcRaw 0.66636386 BRCA2
## 14 0.85400000 0.94463668 0.77777778 819 14 4 48 0.39951811 MutpredScore 0.00000000 BRCA1
## 15 0.00000050 0.64705882 0.76271186 66 45 14 36 0.39489304 LrtScore 0.27371018 BRCA2
## 16 0.99999999 0.75490196 0.61016949 77 36 23 25 0.36260939 GenocanyonScore 0.53286356 BRCA2
## 17 0.94256000 0.45098039 0.89830508 46 53 6 56 0.35990816 FathmmMklCodingScore 0.50315656 BRCA2
## 18 0.16000000 0.77828467 0.89552239 853 60 7 243 0.35769074 AlignGVGDPrior 0.22992242 BRCA1
## 19 0.47500000 0.56862745 0.79661017 58 47 12 44 0.35500288 AlignGVGDPrior 0.52009029 BRCA2
## 20 0.00050000 0.54901961 0.81355932 56 48 11 46 0.35442743 SiftScore 0.25855403 BRCA2
## 21 -1.69500000 0.63725490 0.72881356 65 43 16 37 0.35277752 ProveanScore 0.24861842 BRCA2
## 22 0.82250000 0.77737226 0.88059701 852 59 8 244 0.34928325 Vest3Score 0.28788479 BRCA1
## 23 0.99992050 0.48039216 0.86440678 49 51 8 53 0.34740648 MutationtasterScore 0.49785279 BRCA2
## 24 5.27148350 0.35294118 0.94915254 36 56 3 66 0.33974695 CaddRaw 0.51075749 BRCA2
## 25 0.71700000 0.80200730 0.80597015 879 54 13 217 0.33509124 RevelScore 0.23897527 BRCA1
## 26 0.33291750 0.76003650 0.86567164 833 58 9 263 0.32614139 BayesDel 0.21665934 BRCA1
## 27 0.00950000 0.78102190 0.80597015 856 54 13 240 0.31469609 SiftScore 0.03195874 BRCA1
## 28 0.50056819 0.76459854 0.82089552 838 55 12 258 0.30759802 EigenPcRaw 0.18944944 BRCA1
## 29 0.48704278 0.73540146 0.86567164 806 58 9 290 0.30584511 EigenRaw 0.19559553 BRCA1
## 30 0.99850000 0.76733577 0.80597015 841 54 13 255 0.30242725 Polyphen2HvarScore 0.21799701 BRCA1
## 31 0.62648930 0.73572744 0.85074627 799 57 10 287 0.29987992 MCapScore 0.00000000 BRCA1
## 32 -3.82500000 0.68339416 0.83582090 749 56 11 347 0.25423225 ProveanScore 0.03316140 BRCA1
## 33 0.00030500 0.72262774 0.77611940 792 52 15 304 0.25215137 LrtScore 0.03506381 BRCA1
## 34 0.71682950 0.64689781 0.85074627 709 57 10 387 0.23867426 Gm12878FitconsScore 0.10616048 BRCA1
## 35 0.99950000 0.58850365 0.91044776 645 61 6 451 0.23419384 Polyphen2HdivScore 0.11587771 BRCA1
## 36 0.66725550 0.34313725 0.86440678 35 51 8 67 0.22602741 H1HescFitconsScore 0.32518476 BRCA2
## 37 0.71947300 0.70529197 0.74626866 773 50 17 323 0.22541914 IntegratedFitconsScore 0.12207350 BRCA1
## 38 0.83088500 0.53102190 0.92537313 582 62 5 514 0.21269305 FathmmMklCodingScore 0.10619715 BRCA1
## 39 0.98464723 0.20588235 0.94915254 21 56 3 81 0.20974405 DannScore 0.43303285 BRCA2
## 40 0.64960000 0.69981752 0.71641791 767 48 19 329 0.20720478 MetasvmScore 0.14109121 BRCA1
## 41 0.01255058 0.53010949 0.89552239 581 60 7 515 0.19836006 GenocanyonScore 0.07165259 BRCA1
## 42 5.73541700 0.77098540 0.56716418 845 38 29 251 0.18232528 CaddRaw 0.21501036 BRCA1
## 43 0.77505000 0.61952555 0.71641791 679 48 19 417 0.15979187 MetalrScore 0.15233433 BRCA1
## 44 0.71723900 0.68795620 0.61194030 754 41 26 342 0.14868508 H1HescFitconsScore 0.13435074 BRCA1
## 45 0.67874900 0.25490196 0.86440678 26 51 8 76 0.14085006 IntegratedFitconsScore 0.33394710 BRCA2
## 46 0.99172894 0.40054745 0.80597015 439 54 13 657 0.09871786 DannScore 0.10790486 BRCA1
## 47 -4.01000000 0.32481752 0.85074627 356 57 10 740 0.08808621 FathmmScore 0.06508961 BRCA1
## 48 0.99987900 0.99726277 0.01492537 1093 1 66 3 0.04850747 MutationtasterScore 0.05808745 BRCA1
## 49 0.66945200 0.64705882 0.38983051 66 23 36 36 0.03688933 HuvecFitconsScore 0.34071703 BRCA2
## 50 0.65331700 0.69799270 0.37313433 765 25 42 331 0.03595966 HuvecFitconsScore 0.08734389 BRCA1
## 51 0.71682950 0.04901961 0.96610169 5 57 2 97 0.03572777 Gm12878FitconsScore 0.39562637 BRCA2
## 52 -Inf 1.00000000 0.00000000 102 0 59 0 NaN Polyphen2HdivScore 0.50874078 BRCA2
## 53 Inf 0.00000000 1.00000000 0 59 0 102 NaN Polyphen2HdivScore 0.50874078 BRCA2tmp %>%
ggplot(aes(x=model, y=mcc, fill=Gene)) +
geom_bar(stat='identity') +
facet_grid(Gene~.) +
theme(legend.position = "none") +
theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
ylab('MCC') +
xlab('')
ggsave(filename = paste0(wd,"/results/MCC_plot.png"), width = 14, height = 6, units = "in", dpi = 300)Save table S2.
write.table(rbind(b1_PREDICTIONS, b2_PREDICTIONS), file='results/TableS2.tsv', sep='\t', row.names = FALSE)save.image(file="working/v3.4.RData")